diff --git a/.editorconfig b/.editorconfig
index 7a3ba6aad0..11c1681bad 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,9 +8,6 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{yml,yaml}]
-indent_size = 2
-
 # These files are edited upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
index 191fabd22a..afa1a525c0 100644
--- a/.github/.dockstore.yml
+++ b/.github/.dockstore.yml
@@ -1,6 +1,6 @@
 # Dockstore config version, not pipeline version
 version: 1.2
 workflows:
-  - subclass: nfl
-    primaryDescriptorPath: /nextflow.config
-    publish: True
+    -   subclass: nfl
+        primaryDescriptorPath: /nextflow.config
+        publish: True
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
index 2d21d897da..19231b7d4a 100644
--- a/.github/ISSUE_TEMPLATE/config.yml
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,8 +1,8 @@
 blank_issues_enabled: false
 contact_links:
-  - name: Join nf-core
-    url: https://nf-co.re/join
-    about: Please join the nf-core community here
-  - name: "Slack #rnaseq channel"
-    url: https://nfcore.slack.com/channels/rnaseq
-    about: Discussion about the nf-core/rnaseq pipeline
+    -   name: Join nf-core
+        url: https://nf-co.re/join
+        about: Please join the nf-core community here
+    -   name: "Slack #rnaseq channel"
+        url: https://nfcore.slack.com/channels/rnaseq
+        about: Discussion about the nf-core/rnaseq pipeline
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 2c312b797f..dc42b89667 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -4,41 +4,41 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
-  workflow_dispatch:
+    release:
+        types: [published]
+    workflow_dispatch:
 
 env:
-  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+    AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+    AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+    TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+    AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+    AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+    AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
 
 jobs:
-  run-awstest:
-    name: Run AWS full tests
-    if: github.repository == 'nf-core/rnaseq'
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        aligner: ['star_salmon', 'star_rsem', 'hisat2']
-    steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        # Do a full-scale run with each of the three aligners
-        run: |
-          aws batch submit-job \
-            --region eu-west-1 \
-            --job-name nf-core-rnaseq \
-            --job-queue $AWS_JOB_QUEUE \
-            --job-definition $AWS_JOB_DEFINITION \
-            --container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test_full --aligner '"${{matrix.aligner}}"' --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"'/aligner_'"${{matrix.aligner}}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"'/'"${{matrix.aligner}}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+    run-awstest:
+        name: Run AWS full tests
+        if: github.repository == 'nf-core/rnaseq'
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                aligner: ['star_salmon', 'star_rsem', 'hisat2']
+        steps:
+            -   name: Setup Miniconda
+                uses: conda-incubator/setup-miniconda@v2
+                with:
+                    auto-update-conda: true
+                    python-version: 3.7
+            -   name: Install awscli
+                run: conda install -c conda-forge awscli
+            -   name: Start AWS batch job
+                # Do a full-scale run with each of the three aligners
+                run: |
+                    aws batch submit-job \
+                        --region eu-west-1 \
+                        --job-name nf-core-rnaseq \
+                        --job-queue $AWS_JOB_QUEUE \
+                        --job-definition $AWS_JOB_DEFINITION \
+                        --container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test_full --aligner '"${{matrix.aligner}}"' --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"'/aligner_'"${{matrix.aligner}}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"'/'"${{matrix.aligner}}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
 
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 4cfdee6e76..3a3e91d719 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -4,34 +4,34 @@ name: nf-core AWS test
 # It runs the -profile 'test' on AWS batch.
 
 on:
-  workflow_dispatch:
+    workflow_dispatch:
 
 env:
-  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+    AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+    AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+    TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+    AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+    AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+    AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
 
 jobs:
-  run-awstest:
-    name: Run AWS tests
-    if: github.repository == 'nf-core/rnaseq'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        run: |
-          aws batch submit-job \
-          --region eu-west-1 \
-          --job-name nf-core-rnaseq \
-          --job-queue $AWS_JOB_QUEUE \
-          --job-definition $AWS_JOB_DEFINITION \
-          --container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+    run-awstest:
+        name: Run AWS tests
+        if: github.repository == 'nf-core/rnaseq'
+        runs-on: ubuntu-latest
+        steps:
+            -   name: Setup Miniconda
+                uses: conda-incubator/setup-miniconda@v2
+                with:
+                    auto-update-conda: true
+                    python-version: 3.7
+            -   name: Install awscli
+                run: conda install -c conda-forge awscli
+            -   name: Start AWS batch job
+                run: |
+                    aws batch submit-job \
+                    --region eu-west-1 \
+                    --job-name nf-core-rnaseq \
+                    --job-queue $AWS_JOB_QUEUE \
+                    --job-definition $AWS_JOB_DEFINITION \
+                    --container-overrides '{"command": ["nf-core/rnaseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/rnaseq/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/rnaseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 3f0ef0d769..6ad9d55c85 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -2,45 +2,45 @@ name: nf-core branch protection
 # This workflow is triggered on PRs to master branch on the repository
 # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
-  pull_request_target:
-    branches: [master]
+    pull_request_target:
+        branches: [master]
 
 jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
-      - name: Check PRs
-        if: github.repository == 'nf-core/rnaseq'
-        run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnaseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
-
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## This PR is against the `master` branch :x:
-
-            * Do not close this PR
-            * Click _Edit_ and change the `base` to `dev`
-            * This CI test will remain failed until you push a new commit
-
-            ---
-
-            Hi @${{ github.event.pull_request.user.login }},
-
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
-
-            You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
-            Note that even after this, the test will continue to show as failing until you push a new commit.
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+    test:
+        runs-on: ubuntu-latest
+        steps:
+            # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+            -   name: Check PRs
+                if: github.repository == 'nf-core/rnaseq'
+                run: |
+                    { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnaseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+
+
+            # If the above check failed, post a comment on the PR explaining the failure
+            # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+            -   name: Post PR comment
+                if: failure()
+                uses: mshick/add-pr-comment@v1
+                with:
+                    message: |
+                        ## This PR is against the `master` branch :x:
+
+                        * Do not close this PR
+                        * Click _Edit_ and change the `base` to `dev`
+                        * This CI test will remain failed until you push a new commit
+
+                        ---
+
+                        Hi @${{ github.event.pull_request.user.login }},
+
+                        It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
+                        The `master` branch on nf-core repositories should always contain code from the latest release.
+                        Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+
+                        You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+                        Note that even after this, the test will continue to show as failing until you push a new commit.
+
+                        Thanks again for your contribution!
+                    repo-token: ${{ secrets.GITHUB_TOKEN }}
+                    allow-repeats: false
 
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4ca2a861ab..38699303e4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,168 +1,168 @@
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  push:
-    branches:
-      - dev
-  pull_request:
-  release:
-    types: [published]
+    push:
+        branches:
+            - dev
+    pull_request:
+    release:
+        types: [published]
 
 jobs:
-  test:
-    name: Run workflow tests
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ matrix.nxf_ver }}
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['21.04.0']
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
-
-  star_salmon:
-    name: Test STAR Salmon with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '21.04.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        parameters:
-          - '--skip_qc'
-          - '--remove_ribo_rna'
-          - '--skip_trimming'
-          - '--gtf false'
-          - '--star_index false'
-          - '--transcript_fasta false'
-          - '--min_mapped_reads 90'
-          - '--with_umi'
-          - '--with_umi --skip_trimming'
-          - '--bam_csi_index'
-          - '--save_align_intermeds --save_reference'
-          - '--featurecounts_group_type false'
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with STAR and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }}
-
-  star_rsem:
-    name: Test STAR RSEM with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '21.04.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        parameters:
-          - '--skip_qc'
-          - '--rsem_index false'
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
+    test:
+        name: Run workflow tests
+        # Only run on push if this is the nf-core dev branch (merged PRs)
+        if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+        runs-on: ubuntu-latest
         env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with RSEM STAR and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }}
-
-  hisat2:
-    name: Test HISAT2 with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '21.04.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        parameters:
-          - '--skip_qc'
-          - '--hisat2_index false'
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with HISAT2 and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }}
-
-  salmon:
-    name: Test Salmon with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '21.04.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        parameters:
-          - '--skip_qc --skip_alignment'
-          - '--salmon_index false --transcript_fasta false'
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with Salmon and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }}
-
-  sra_download:
-    name: Test downloading of public data
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '21.04.0'
-      NXF_ANSI_LOG: false
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline to download public data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_sra,docker
+            NXF_VER: ${{ matrix.nxf_ver }}
+            NXF_ANSI_LOG: false
+        strategy:
+            matrix:
+                # Nextflow versions: check pipeline minimum and current latest
+                nxf_ver: ['21.04.0']
+        steps:
+            -   name: Check out pipeline code
+                uses: actions/checkout@v2
+
+            -   name: Install Nextflow
+                run: |
+                    wget -qO- get.nextflow.io | bash
+                    sudo mv nextflow /usr/local/bin/
+
+            -   name: Run pipeline with test data
+                run: |
+                    nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+
+    star_salmon:
+        name: Test STAR Salmon with workflow parameters
+        if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+        runs-on: ubuntu-latest
+        env:
+            NXF_VER: '21.04.0'
+            NXF_ANSI_LOG: false
+        strategy:
+            matrix:
+                parameters:
+                    - '--skip_qc'
+                    - '--remove_ribo_rna'
+                    - '--skip_trimming'
+                    - '--gtf false'
+                    - '--star_index false'
+                    - '--transcript_fasta false'
+                    - '--min_mapped_reads 90'
+                    - '--with_umi'
+                    - '--with_umi --skip_trimming'
+                    - '--bam_csi_index'
+                    - '--save_align_intermeds --save_reference'
+                    - '--featurecounts_group_type false'
+        steps:
+            -   name: Check out pipeline code
+                uses: actions/checkout@v2
+
+            -   name: Install Nextflow
+                run: |
+                    wget -qO- get.nextflow.io | bash
+                    sudo mv nextflow /usr/local/bin/
+
+            -   name: Run pipeline with STAR and various parameters
+                run: |
+                    nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }}
+
+    star_rsem:
+        name: Test STAR RSEM with workflow parameters
+        if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+        runs-on: ubuntu-latest
+        env:
+            NXF_VER: '21.04.0'
+            NXF_ANSI_LOG: false
+        strategy:
+            matrix:
+                parameters:
+                    - '--skip_qc'
+                    - '--rsem_index false'
+        steps:
+            -   name: Check out pipeline code
+                uses: actions/checkout@v2
+
+            -   name: Install Nextflow
+                env:
+                    CAPSULE_LOG: none
+                run: |
+                    wget -qO- get.nextflow.io | bash
+                    sudo mv nextflow /usr/local/bin/
+
+            -   name: Run pipeline with RSEM STAR and various parameters
+                run: |
+                    nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }}
+
+    hisat2:
+        name: Test HISAT2 with workflow parameters
+        if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+        runs-on: ubuntu-latest
+        env:
+            NXF_VER: '21.04.0'
+            NXF_ANSI_LOG: false
+        strategy:
+            matrix:
+                parameters:
+                    - '--skip_qc'
+                    - '--hisat2_index false'
+        steps:
+            -   name: Check out pipeline code
+                uses: actions/checkout@v2
+
+            -   name: Install Nextflow
+                run: |
+                    wget -qO- get.nextflow.io | bash
+                    sudo mv nextflow /usr/local/bin/
+
+            -   name: Run pipeline with HISAT2 and various parameters
+                run: |
+                    nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }}
+
+    salmon:
+        name: Test Salmon with workflow parameters
+        if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+        runs-on: ubuntu-latest
+        env:
+            NXF_VER: '21.04.0'
+            NXF_ANSI_LOG: false
+        strategy:
+            matrix:
+                parameters:
+                    - '--skip_qc --skip_alignment'
+                    - '--salmon_index false --transcript_fasta false'
+        steps:
+            -   name: Check out pipeline code
+                uses: actions/checkout@v2
+
+            -   name: Install Nextflow
+                run: |
+                    wget -qO- get.nextflow.io | bash
+                    sudo mv nextflow /usr/local/bin/
+
+            -   name: Run pipeline with Salmon and various parameters
+                run: |
+                    nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }}
+
+    sra_download:
+        name: Test downloading of public data
+        if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+        runs-on: ubuntu-latest
+        env:
+            NXF_VER: '21.04.0'
+            NXF_ANSI_LOG: false
+        steps:
+            -   name: Check out pipeline code
+                uses: actions/checkout@v2
+
+            -   name: Install Nextflow
+                run: |
+                    wget -qO- get.nextflow.io | bash
+                    sudo mv nextflow /usr/local/bin/
+
+            -   name: Run pipeline to download public data
+                run: |
+                    nextflow run ${GITHUB_WORKSPACE} -profile test_sra,docker
 
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 554e1154dd..fefb7664fb 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -2,148 +2,148 @@ name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
 # It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
 on:
-  push:
-  pull_request:
-  release:
-    types: [published]
+    push:
+    pull_request:
+    release:
+        types: [published]
 
 jobs:
 
-  Markdown:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
-      - name: Install markdownlint
-        run: npm install -g markdownlint-cli
-      - name: Run Markdownlint
-        run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## Markdown linting is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install `markdownlint-cli`
-                * On Mac: `brew install markdownlint-cli`
-                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
-            * Fix the markdown errors
-                * Automatically: `markdownlint . --config .github/markdownlint.yml --fix`
-                * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-
-            We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-
-  EditorConfig:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: actions/setup-node@v1
-        with:
-          node-version: "10"
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
-
-  YAML:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
-        with:
-          node-version: '10'
-      - name: Install yaml-lint
-        run: npm install -g yaml-lint
-      - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## YAML linting is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install `yaml-lint`
-                * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
-            * Fix the markdown errors
-                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
-                * Fix any reported errors in your YAML files
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-
-            We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-
-
-  nf-core:
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: 21.03.0-edge
-    steps:
-
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
+    Markdown:
+        runs-on: ubuntu-latest
+        steps:
+            -   uses: actions/checkout@v2
+            -   uses: actions/setup-node@v1
+                with:
+                    node-version: '10'
+            -   name: Install markdownlint
+                run: npm install -g markdownlint-cli
+            -   name: Run Markdownlint
+                run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+
+            # If the above check failed, post a comment on the PR explaining the failure
+            -   name: Post PR comment
+                if: failure()
+                uses: mshick/add-pr-comment@v1
+                with:
+                    message: |
+                        ## Markdown linting is failing
+
+                        To keep the code consistent with lots of contributors, we run automated code consistency checks.
+                        To fix this CI test, please run:
+
+                        * Install `markdownlint-cli`
+                                * On Mac: `brew install markdownlint-cli`
+                                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
+                        * Fix the markdown errors
+                                * Automatically: `markdownlint . --config .github/markdownlint.yml --fix`
+                                * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`
+
+                        Once you push these changes the test should pass, and you can hide this comment :+1:
+
+                        We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+                        Thanks again for your contribution!
+                    repo-token: ${{ secrets.GITHUB_TOKEN }}
+                    allow-repeats: false
+
+    EditorConfig:
+        runs-on: ubuntu-latest
+        steps:
+            -   uses: actions/checkout@v2
+
+            -   uses: actions/setup-node@v1
+                with:
+                    node-version: "10"
+
+            -   name: Install editorconfig-checker
+                run: npm install -g editorconfig-checker
+
+            -   name: Run ECLint check
+                run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
+
+    YAML:
+        runs-on: ubuntu-latest
+        steps:
+            -   uses: actions/checkout@v1
+            -   uses: actions/setup-node@v1
+                with:
+                    node-version: '10'
+            -   name: Install yaml-lint
+                run: npm install -g yaml-lint
+            -   name: Run yaml-lint
+                run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
+
+            # If the above check failed, post a comment on the PR explaining the failure
+            -   name: Post PR comment
+                if: failure()
+                uses: mshick/add-pr-comment@v1
+                with:
+                    message: |
+                        ## YAML linting is failing
+
+                        To keep the code consistent with lots of contributors, we run automated code consistency checks.
+                        To fix this CI test, please run:
+
+                        * Install `yaml-lint`
+                                * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
+                        * Fix the markdown errors
+                                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
+                                * Fix any reported errors in your YAML files
+
+                        Once you push these changes the test should pass, and you can hide this comment :+1:
+
+                        We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+                        Thanks again for your contribution!
+                    repo-token: ${{ secrets.GITHUB_TOKEN }}
+                    allow-repeats: false
+
+
+    nf-core:
+        runs-on: ubuntu-latest
         env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - uses: actions/setup-python@v1
-        with:
-          python-version: '3.6'
-          architecture: 'x64'
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core
-
-      - name: Run nf-core lint
-        env:
-          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE} --markdown lint_results.md
-
-      - name: Save PR number
-        if: ${{ always() }}
-        run: echo ${{ github.event.pull_request.number }} > PR_number.txt
-
-      - name: Upload linting log file artifact
-        if: ${{ always() }}
-        uses: actions/upload-artifact@v2
-        with:
-          name: linting-logs
-          path: |
-            lint_log.txt
-            lint_results.md
-            PR_number.txt
+            NXF_VER: 21.03.0-edge
+        steps:
+
+            -   name: Check out pipeline code
+                uses: actions/checkout@v2
+
+            -   name: Install Nextflow
+                env:
+                    CAPSULE_LOG: none
+                run: |
+                    wget -qO- get.nextflow.io | bash
+                    sudo mv nextflow /usr/local/bin/
+
+            -   uses: actions/setup-python@v1
+                with:
+                    python-version: '3.6'
+                    architecture: 'x64'
+
+            -   name: Install dependencies
+                run: |
+                    python -m pip install --upgrade pip
+                    pip install nf-core
+
+            -   name: Run nf-core lint
+                env:
+                    GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+                    GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+                    GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+                run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE} --markdown lint_results.md
+
+            -   name: Save PR number
+                if: ${{ always() }}
+                run: echo ${{ github.event.pull_request.number }} > PR_number.txt
+
+            -   name: Upload linting log file artifact
+                if: ${{ always() }}
+                uses: actions/upload-artifact@v2
+                with:
+                    name: linting-logs
+                    path: |
+                        lint_log.txt
+                        lint_results.md
+                        PR_number.txt
 
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 90f03c6f91..ae2d53b003 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -4,26 +4,26 @@ name: nf-core linting comment
 # It posts an automated comment to the PR, even if the PR is coming from a fork
 
 on:
-  workflow_run:
-    workflows: ["nf-core linting"]
+    workflow_run:
+        workflows: ["nf-core linting"]
 
 jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Download lint results
-        uses: dawidd6/action-download-artifact@v2
-        with:
-          workflow: linting.yml
+    test:
+        runs-on: ubuntu-latest
+        steps:
+            -   name: Download lint results
+                uses: dawidd6/action-download-artifact@v2
+                with:
+                    workflow: linting.yml
 
-      - name: Get PR number
-        id: pr_number
-        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+            -   name: Get PR number
+                id: pr_number
+                run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
 
-      - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@v2
-        with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          number: ${{ steps.pr_number.outputs.pr_number }}
-          path: linting-logs/lint_results.md
+            -   name: Post PR comment
+                uses: marocchino/sticky-pull-request-comment@v2
+                with:
+                    GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+                    number: ${{ steps.pr_number.outputs.pr_number }}
+                    path: linting-logs/lint_results.md
 
diff --git a/.markdownlint.yml b/.markdownlint.yml
index b5c4bbf8a3..9e605fcfab 100644
--- a/.markdownlint.yml
+++ b/.markdownlint.yml
@@ -2,13 +2,13 @@
 default: true
 line-length: false
 ul-indent:
-  indent: 4
+    indent: 4
 no-duplicate-header:
-  siblings_only: true
+    siblings_only: true
 no-inline-html:
     allowed_elements:
-      - img
-      - p
-      - kbd
-      - details
-      - summary
+        - img
+        - p
+        - kbd
+        - details
+        - summary
diff --git a/.nf-core-lint.yaml b/.nf-core-lint.yaml
index 058afd8ab5..e04895a992 100644
--- a/.nf-core-lint.yaml
+++ b/.nf-core-lint.yaml
@@ -1,10 +1,10 @@
 files_unchanged:
-  - .github/PULL_REQUEST_TEMPLATE.md
-  - .github/workflows/linting.yml
-  - assets/email_template.html
-  - assets/email_template.txt
-  - assets/multiqc_config.yaml
-  - lib/NfcoreSchema.groovy
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/linting.yml
+    - assets/email_template.html
+    - assets/email_template.txt
+    - assets/multiqc_config.yaml
+    - lib/NfcoreSchema.groovy
 files_exist:
-  - bin/markdown_to_html.py
+    - bin/markdown_to_html.py
 actions_awsfulltest: False